...He says the universe is not perfect. For example, squids have better eyes than human beings. I don't think that this argument in any way disproves God's existence. Let me mention three reasons. First, that objection assumes a static theory of creation--that God created each individual creature, which never changes. But even creationists typically hold to a dynamic theory of creation which allows micro-evolutionary change within certain types, so that God could create a certain primal type of being and then there would be micro-evolutionary change within that type, and you might look at these sorts of imperfections (as he calls them) as by-products of micro-evolutionary pressures which gradually emerge.

Secondly, the objection presumes to know what God would do if He were to design something, that we know that God would create the eye in a certain way if He existed or He would create the digestive system in this way if He existed. And I personally think that's simply presumptuous. We have no idea how to speculate about what God would create if He were to exist. Maybe it's not important to God that we be able to have eyes to see in exactly a certain way, maybe there are other off-setting reasons why God permits systems designed in this way to exist. In other words, the argument is enormously presumptuous in thinking that we know what God would create if He were to exist.

And thirdly, perfection is a relative term, after all. These supposedly imperfect organs like the human eye function extraordinarily well. I mean, think of what the human eye has done in terms of art, literature, architecture, and so forth! This is hardly persuasive evidence, I think, that it could not be the product of an intelligent designer.

In fact, that leads me to his other argument, concerning biological evolution. And I'm going to suggest that the idea that evolution could have occurred without an intelligent Designer is so improbable as to be fantastic. This has been demonstrated by Barrowand Tipler in their book The Anthropic Cosmological Principle. In this book, they list ten steps in the course of human evolution, each of which is so improbable that before it would have occurred the sun would have ceased to be a main sequence star and would have burned up the earth.19 They estimate the odds of the evolution of the human genome by chance to be on the order of 4-360 (110,000), a number which is so huge that to call it astronomical would be a wild understatement. In other words, if evolution did occur, it would have been a miracle, so that evolution is actually evidence for the existence of God! And here the Christian can be much more open to where the evidence leads. He could say, "Well, God could have used evolution; He could have used special creation. I'm open to the evidence." But, you see, for the naturalist evolution is the only game in town! No matter how fantastic the odds, no matter how improbable the evidence, he's stuck with it because he hasn't got an intelligent Designer. So it seems to me that the Christian can be far more objective on this point. After all, if you were to find watch lying on the ground, and, say, it didn't function exactly perfectly, it lost one minute per hour, would you therefore conclude that the watch was not designed properly?

WLC in a Response To A Question About His Debate With Ayala:

First, consider the issue of design flaws in nature. There are a number of ways in which the Christian theologian might successfully respond to this problem. He might challenge the assumption that these supposed flaws are really flaws at all. Take, for example, the claim that the placement of the optic nerve in the human eye is flawed because it results in a small blind spot in our visual field. Might God have a good biological reason for so designing the eye? Yes, indeed! As Michael Denton explains, the difference in the placement of the optic nerve in the human eye in comparison with cephalopod eyes is because of the need for the greater supply of oxygen for high-acuity vision in warm-blooded animals. According to Denton, "Rather than being a case of maladaptation, the inverted retina is probably an essential element in the overall design of the vertebrate visual system" (personal communication). So this alleged flaw turns out not to be a flaw at all. Over and over again, we have found that what appeared at first to be design flaws have, with greater understanding, turned out not to be flaws at all.

But suppose, for the sake of argument, that the flaws do seem to be real and suggest that some particular feature is a result of natural selection. Fine! Such a conclusion would be troubling only for someone who espouses a highly restricted form of special creationism, which held that God created every individual species exactly as it is today. But even special creationists typically don't hold to such a restrictive view. They usually hold that the "kinds" created by God in Genesis 1 were on the biological level of the order or family, and that evolution took over from there. So, for example, God created the common ancestor of the family Ursidae or the bear family, which has since evolved into eight different species of bears. It's hardly surprising, then, that the so-called "Panda's thumb," often touted as a design flaw, should have evolved in one species of bear, the Pandas. And it hardly needs to be said that theologians who don't hold to special creationism but embrace the thesis of common ancestry are not at all surprised that organisms should bear the design imprint of their ancestors. Many of the so-called flaws are just tip-offs to common ancestry. So I don't think supposed design flaws are a very serious theological problem at all.

...Designs exhibit various levels of optimality, and there's no reason to restrict design inferences to only maximally optimal designs. In fact, it would be positively foolish to do so. If a biological system meets William Dembski's criteria for being designed (high improbability plus conformity to an independently given pattern), that design inference is not nullified by the possibility of structures which could have been better designed. ...So suppose, for example, that the Christian theologian responds to this objection by saying that God could have independent motives for designing a world with less than optimal structures in it.

Of course, the question still remains, for both Ayala and me, why did God create a world featuring an evolutionary prelude to the appearance of man? I suspect that the answer to that question will have to do with God's ultimate purposes for human beings, for the creation of an ecosystem where autonomous human agents can flourish and choose without coercion to embrace or reject God's offer of saving grace and a personal relationship with Himself.

--My own two cents on this (how every unique and wild) is: I think evolution may plausibly be metaphysically necessary as a means of 'creation' since there aren't any laws of nature in biology which probably means that biological organisms do not have essences, and if on one construal of what a law of nature amounts to derives from things having an essence, then it seems that God may have had no choice so to speak but to create biological life in 'real time' as opposed to creating life on Earth ex nihilo.

--This is taken from the Reasonstobelieve crew...They offer scientific responses to various examples of alleged 'poor designs.' I consider certain of these articles to be partial answers only whereas others are plausible on the whole, but I leave it to the reader to decide: